On Fri, Oct 25, 2013 at 11:45 AM, Petri Kursula
What I saw were problems with phenix.refine (well-did not try anything else yet). The job seems to start normally (no error messages), but when you check the log file, nothing is happening (it remains empty or stops at initial steps). If you abort, close Phenix and restart it, the exactly same job runs just fine. I’m starting Phenix GUI from ‘Applications’, not command line.
Can you either a) try starting on the command line (/Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/bin/phenix) and looking for console output, or b) open the Console app and see what is printed out? I suspect it will have an error message involving "malloc", because that's what happens to be sometimes. (Always with either phenix.refine or phenix.maps.) As far as I can tell this is some kind of very low-level error in either Python or the compiler used to build Phenix - as you note, it is not consistently reproducible either, and it doesn't seem to be correlated with any specific model or data issues that I can see. -Nat